A multi-chromatogram MRM feature. More...
#include <OpenMS/KERNEL/MRMFeature.h>
Inheritance diagram for MRMFeature:
Public Types | |
| typedef std::vector< Feature > | FeatureListType |
| Type definitions. More... | |
| typedef std::map< String, double > | PGScoresType |
| Peak group score type. More... | |
 Public Types inherited from Feature | |
| typedef QualityLess | OverallQualityLess |
| Compare by quality. More... | |
| Public Types inherited from BaseFeature | |
| enum | AnnotationState { FEATURE_ID_NONE, FEATURE_ID_SINGLE, FEATURE_ID_MULTIPLE_SAME, FEATURE_ID_MULTIPLE_DIVERGENT, SIZE_OF_ANNOTATIONSTATE } |
| state of identification, use getIDState() to query it More... | |
| typedef float | QualityType |
| Type of quality values. More... | |
| typedef Int | ChargeType |
| Type of charge values. More... | |
| typedef float | WidthType |
| Type of feature width/FWHM (RT) More... | |
| Public Types inherited from Peak2D | |
| typedef float | IntensityType |
| Intensity type. More... | |
| typedef double | CoordinateType |
| Coordinate type (of the position) More... | |
| typedef DPosition< 2 > | PositionType |
| Position type. More... | |
| enum | DimensionDescription { RT = 0, MZ = 1, DIMENSION = 2 } |
| This enum maps the symbolic names of the dimensions to numbers. More... | |
| Public Types inherited from UniqueIdInterface | |
| enum | { INVALID = 0 } |
| This is the invalid unique id (cast it to a UInt64 if you like) More... | |
Public Member Functions | |
Constructors and Destructor | |
| MRMFeature () | |
| Default constructor. More... | |
| MRMFeature (const MRMFeature &rhs) | |
| Copy constructor. More... | |
| MRMFeature & | operator= (const MRMFeature &rhs) |
| Assignment operator. More... | |
| virtual | ~MRMFeature () |
| Destructor. More... | |
Accessors | |
| const PGScoresType & | getScores () const |
| get all peakgroup scores More... | |
| double | getScore (const String &score_name) |
| get a single peakgroup score More... | |
| Feature & | getFeature (String key) |
| get a specified feature More... | |
| void | setScores (const PGScoresType &scores) |
| set all peakgroup scores More... | |
| void | addScore (const String &score_name, double score) |
| set a single peakgroup score More... | |
| void | addFeature (Feature &feature, const String &key) |
| Adds an feature from a single chromatogram into the feature. More... | |
| const std::vector< Feature > & | getFeatures () const |
| get a list of features More... | |
| void | getFeatureIDs (std::vector< String > &result) const |
| get a list of IDs of available features More... | |
| void | addPrecursorFeature (Feature &feature, const String &key) |
| Adds a precursor feature from a single chromatogram into the feature. More... | |
| void | getPrecursorFeatureIDs (std::vector< String > &result) const |
| get a list of IDs of available precursor features More... | |
| Feature & | getPrecursorFeature (String key) |
| get a specified precursor feature More... | |
| Public Member Functions inherited from Feature | |
| Feature & | operator= (const Feature &rhs) |
| Assignment operator. More... | |
| bool | operator== (const Feature &rhs) const |
| Equality operator. More... | |
| const std::vector< Feature > & | getSubordinates () const |
| immutable access to subordinate features More... | |
| std::vector< Feature > & | getSubordinates () |
| mutable access to subordinate features More... | |
| void | setSubordinates (const std::vector< Feature > &rhs) |
| mutable access to subordinate features More... | |
| template<typename Type > | |
| Size | applyMemberFunction (Size(Type::*member_function)()) |
| Applies a member function of Type to the feature (including subordinates). The returned values are accumulated. More... | |
| template<typename Type > | |
| Size | applyMemberFunction (Size(Type::*member_function)() const) const |
| The "const" variant. More... | |
| Feature () | |
| Default constructor. More... | |
| Feature (const Feature &feature) | |
| Copy constructor. More... | |
| ~Feature () | |
| Destructor. More... | |
| const std::vector< ConvexHull2D > & | getConvexHulls () const |
| Non-mutable access to the convex hulls. More... | |
| std::vector< ConvexHull2D > & | getConvexHulls () |
| Mutable access to the convex hulls of single mass traces. More... | |
| void | setConvexHulls (const std::vector< ConvexHull2D > &hulls) |
| Set the convex hulls of single mass traces. More... | |
| ConvexHull2D & | getConvexHull () const |
| Returns the overall convex hull of the feature (calculated from the convex hulls of the mass traces) More... | |
| bool | encloses (double rt, double mz) const |
Returns if the mass trace convex hulls of the feature enclose the position specified by rt and mz. More... | |
| QualityType | getOverallQuality () const |
| Non-mutable access to the overall quality. More... | |
| void | setOverallQuality (QualityType q) |
| Set the overall quality. More... | |
| QualityType | getQuality (Size index) const |
| Non-mutable access to the quality in dimension c. More... | |
| void | setQuality (Size index, QualityType q) |
| Set the quality in dimension c. More... | |
| Public Member Functions inherited from BaseFeature | |
| WidthType | getWidth () const |
| Non-mutable access to the features width (full width at half max, FWHM) More... | |
| void | setWidth (WidthType fwhm) |
| Set the width of the feature (FWHM) More... | |
| const ChargeType & | getCharge () const |
| Non-mutable access to charge state. More... | |
| void | setCharge (const ChargeType &ch) |
| Set charge state. More... | |
| BaseFeature & | operator= (const BaseFeature &rhs) |
| Assignment operator. More... | |
| bool | operator== (const BaseFeature &rhs) const |
| Equality operator. More... | |
| bool | operator!= (const BaseFeature &rhs) const |
| Inequality operator. More... | |
| const std::vector< PeptideIdentification > & | getPeptideIdentifications () const |
| returns a const reference to the PeptideIdentification vector More... | |
| std::vector< PeptideIdentification > & | getPeptideIdentifications () |
| returns a mutable reference to the PeptideIdentification vector More... | |
| void | setPeptideIdentifications (const std::vector< PeptideIdentification > &peptides) |
| sets the PeptideIdentification vector More... | |
| AnnotationState | getAnnotationState () const |
| state of peptide identifications attached to this feature. If one ID has multiple hits, the output depends on the top-hit only More... | |
| BaseFeature () | |
| Default constructor. More... | |
| BaseFeature (const BaseFeature &feature) | |
| Copy constructor. More... | |
| BaseFeature (const Peak2D &point) | |
| Constructor from raw data point. More... | |
| BaseFeature (const RichPeak2D &point) | |
| Constructor from raw data point with meta information. More... | |
| ~BaseFeature () | |
| Destructor. More... | |
| QualityType | getQuality () const |
| Non-mutable access to the overall quality. More... | |
| void | setQuality (QualityType q) |
| Set the overall quality. More... | |
| Public Member Functions inherited from RichPeak2D | |
| RichPeak2D () | |
| Default constructor. More... | |
| RichPeak2D (const RichPeak2D &p) | |
| Copy constructor. More... | |
| RichPeak2D (const Peak2D &p) | |
| Constructor from Peak2D. More... | |
| RichPeak2D (const PositionType &pos, const IntensityType in) | |
| Member constructor. More... | |
| ~RichPeak2D () | |
| Destructor. More... | |
| RichPeak2D & | operator= (const RichPeak2D &rhs) |
| Assignment operator. More... | |
| RichPeak2D & | operator= (const Peak2D &rhs) |
| Assignment operator. More... | |
| bool | operator== (const RichPeak2D &rhs) const |
| Equality operator. More... | |
| bool | operator!= (const RichPeak2D &rhs) const |
| Equality operator. More... | |
| Public Member Functions inherited from Peak2D | |
| Peak2D & | operator= (const Peak2D &rhs) |
| Assignment operator. More... | |
| bool | operator== (const Peak2D &rhs) const |
| Equality operator. More... | |
| bool | operator!= (const Peak2D &rhs) const |
| Equality operator. More... | |
| Peak2D () | |
| Peak2D (const PositionType &pos, const IntensityType in) | |
| Member constructor. More... | |
| Peak2D (const Peak2D &p) | |
| Copy constructor. More... | |
| ~Peak2D () | |
| Destructor. More... | |
| IntensityType | getIntensity () const |
| void | setIntensity (IntensityType intensity) |
| Non-mutable access to the data point intensity (height) More... | |
| PositionType const & | getPosition () const |
| Non-mutable access to the position. More... | |
| PositionType & | getPosition () |
| Mutable access to the position. More... | |
| void | setPosition (const PositionType &position) |
| Mutable access to the position. More... | |
| CoordinateType | getMZ () const |
| Returns the m/z coordinate (index 1) More... | |
| void | setMZ (CoordinateType coordinate) |
| Mutable access to the m/z coordinate (index 1) More... | |
| CoordinateType | getRT () const |
| Returns the RT coordinate (index 0) More... | |
| void | setRT (CoordinateType coordinate) |
| Mutable access to the RT coordinate (index 0) More... | |
| Public Member Functions inherited from MetaInfoInterface | |
| MetaInfoInterface () | |
| Constructor. More... | |
| MetaInfoInterface (const MetaInfoInterface &rhs) | |
| Copy constructor. More... | |
| ~MetaInfoInterface () | |
| Destructor. More... | |
| MetaInfoInterface & | operator= (const MetaInfoInterface &rhs) |
| Assignment operator. More... | |
| bool | operator== (const MetaInfoInterface &rhs) const |
| Equality operator. More... | |
| bool | operator!= (const MetaInfoInterface &rhs) const |
| Equality operator. More... | |
| const DataValue & | getMetaValue (const String &name) const |
| Returns the value corresponding to a string (or DataValue::EMPTY if not found) More... | |
| const DataValue & | getMetaValue (UInt index) const |
| Returns the value corresponding to an index (or DataValue::EMPTY if not found) More... | |
| bool | metaValueExists (const String &name) const |
| Returns whether an entry with the given name exists. More... | |
| bool | metaValueExists (UInt index) const |
| Returns whether an entry with the given index exists. More... | |
| void | setMetaValue (const String &name, const DataValue &value) |
| Sets the DataValue corresponding to a name. More... | |
| void | setMetaValue (UInt index, const DataValue &value) |
| Sets the DataValue corresponding to an index. More... | |
| void | removeMetaValue (const String &name) |
Removes the DataValue corresponding to name if it exists. More... | |
| void | removeMetaValue (UInt index) |
Removes the DataValue corresponding to index if it exists. More... | |
| void | getKeys (std::vector< String > &keys) const |
| Fills the given vector with a list of all keys for which a value is set. More... | |
| void | getKeys (std::vector< UInt > &keys) const |
| Fills the given vector with a list of all keys for which a value is set. More... | |
| bool | isMetaEmpty () const |
| Returns if the MetaInfo is empty. More... | |
| void | clearMetaInfo () |
| Removes all meta values. More... | |
| Public Member Functions inherited from UniqueIdInterface | |
| UniqueIdInterface () | |
| Default constructor - the unique id will be invalid More... | |
| UniqueIdInterface (const UniqueIdInterface &rhs) | |
| Copy constructor - copies the unique id. More... | |
| UniqueIdInterface & | operator= (UniqueIdInterface const &rhs) |
| Assignment operator - copies the unique id. More... | |
| virtual | ~UniqueIdInterface () |
| Destructor. More... | |
| bool | operator== (UniqueIdInterface const &rhs) const |
| Equality comparison operator - the unique ids must be equal (!) More... | |
| UInt64 | getUniqueId () const |
| Non-mutable access to unique id - returns the unique id. More... | |
| Size | clearUniqueId () |
| Clear the unique id. The new unique id will be invalid. Returns 1 if the unique id was changed, 0 otherwise. More... | |
| void | swap (UniqueIdInterface &from) |
| Size | hasValidUniqueId () const |
| Returns whether the unique id is valid. Returns 1 if the unique id is valid, 0 otherwise. More... | |
| Size | hasInvalidUniqueId () const |
| Returns whether the unique id is invalid. Returns 1 if the unique id is invalid, 0 otherwise. More... | |
| Size | setUniqueId () |
| Assigns a new, valid unique id. Always returns 1. More... | |
| Size | ensureUniqueId () |
| Assigns a valid unique id, but only if the present one is invalid. Returns 1 if the unique id was changed, 0 otherwise. More... | |
| void | setUniqueId (UInt64 rhs) |
| Assigns the given unique id. More... | |
| void | setUniqueId (const String &rhs) |
| Mutable access to unique id. More... | |
Protected Attributes | |
| FeatureListType | features_ |
| FeatureListType | precursor_features_ |
| PGScoresType | pg_scores_ |
| peak group scores More... | |
| std::map< String, int > | feature_map_ |
| map native ids to the features More... | |
| std::map< String, int > | precursor_feature_map_ |
| map native ids to the precursor features More... | |
| Protected Attributes inherited from Feature | |
| QualityType | qualities_ [2] |
| Quality measures for each dimension. More... | |
| std::vector< ConvexHull2D > | convex_hulls_ |
| Array of convex hulls (one for each mass trace) More... | |
| bool | convex_hulls_modified_ |
| Flag that indicates if the overall convex hull needs to be recomputed (i.e. mass trace convex hulls were modified) More... | |
| ConvexHull2D | convex_hull_ |
| Overall convex hull of the feature. More... | |
| std::vector< Feature > | subordinates_ |
| subordinate features (e.g. features that represent alternative explanations, usually with lower quality) More... | |
| Protected Attributes inherited from BaseFeature | |
| QualityType | quality_ |
| Overall quality measure of the feature. More... | |
| ChargeType | charge_ |
| Charge of the peptide represented by this feature. The default value is 0, which represents an unknown charge state. More... | |
| WidthType | width_ |
| Width (FWHM) for the feature. The default value is 0.0, a feature finding algorithm can compute this form the model. More... | |
| std::vector< PeptideIdentification > | peptides_ |
| Peptide PeptideIdentifications belonging to the feature. More... | |
| Protected Attributes inherited from Peak2D | |
| PositionType | position_ |
| The data point position. More... | |
| IntensityType | intensity_ |
| The data point intensity. More... | |
| Protected Attributes inherited from MetaInfoInterface | |
| MetaInfo * | meta_ |
| Pointer to the MetaInfo object (0 by default) More... | |
| Protected Attributes inherited from UniqueIdInterface | |
| UInt64 | unique_id_ |
| the unique id More... | |
Additional Inherited Members | |
| Static Public Member Functions inherited from Peak2D | |
| static char const * | shortDimensionName (UInt const dim) |
| Short name of the dimension (abbreviated form) More... | |
| static char const * | shortDimensionNameRT () |
| Short name of the dimension (abbreviated form) More... | |
| static char const * | shortDimensionNameMZ () |
| Short name of the dimension (abbreviated form) More... | |
| static char const * | fullDimensionName (UInt const dim) |
| Full name of the dimension (self-explanatory form) More... | |
| static char const * | fullDimensionNameRT () |
| Full name of the dimension (self-explanatory form) More... | |
| static char const * | fullDimensionNameMZ () |
| Full name of the dimension (self-explanatory form) More... | |
| static char const * | shortDimensionUnit (UInt const dim) |
| Unit of measurement (abbreviated form) More... | |
| static char const * | shortDimensionUnitRT () |
| Unit of measurement (abbreviated form) More... | |
| static char const * | shortDimensionUnitMZ () |
| Unit of measurement (abbreviated form) More... | |
| static char const * | fullDimensionUnit (UInt const dim) |
| Unit of measurement (self-explanatory form) More... | |
| static char const * | fullDimensionUnitRT () |
| Unit of measurement (self-explanatory form) More... | |
| static char const * | fullDimensionUnitMZ () |
| Unit of measurement (self-explanatory form) More... | |
| Static Public Member Functions inherited from MetaInfoInterface | |
| static MetaInfoRegistry & | metaRegistry () |
| Returns a reference to the MetaInfoRegistry. More... | |
| Static Public Member Functions inherited from UniqueIdInterface | |
| static bool | isValid (UInt64 unique_id) |
| Returns true if the unique_id is valid, false otherwise. More... | |
| Static Public Attributes inherited from BaseFeature | |
| static const std::string | NamesOfAnnotationState [SIZE_OF_ANNOTATIONSTATE] |
| Protected Member Functions inherited from MetaInfoInterface | |
| void | createIfNotExists_ () |
| Creates the MetaInfo object if it does not exist. More... | |
| Static Protected Attributes inherited from Peak2D | |
| static char const *const | dimension_name_short_ [DIMENSION] |
| Short name of the dimension (abbreviated form) More... | |
| static char const *const | dimension_name_full_ [DIMENSION] |
| Full name of the dimension (self-explanatory form) More... | |
| static char const *const | dimension_unit_short_ [DIMENSION] |
| Unit of measurement (abbreviated form) More... | |
| static char const *const | dimension_unit_full_ [DIMENSION] |
| Unit of measurement (self-explanatory form) More... | |
Detailed Description
A multi-chromatogram MRM feature.
An MRM feature contains corresponding features in multiple chromatograms, it is thus a representation of a peak group. The individual features in each chromatogram are represented by OpenMS Features.
Member Typedef Documentation
◆ FeatureListType
| typedef std::vector<Feature> FeatureListType |
Type definitions.
Feature list type
◆ PGScoresType
| typedef std::map<String, double> PGScoresType |
Peak group score type.
Constructor & Destructor Documentation
◆ MRMFeature() [1/2]
| MRMFeature | ( | ) |
Default constructor.
◆ MRMFeature() [2/2]
| MRMFeature | ( | const MRMFeature & | rhs | ) |
Copy constructor.
◆ ~MRMFeature()
|
virtual |
Destructor.
Member Function Documentation
◆ addFeature()
Adds an feature from a single chromatogram into the feature.
Referenced by MRMTransitionGroup< SpectrumT, TransitionT >::subset().
◆ addPrecursorFeature()
Adds a precursor feature from a single chromatogram into the feature.
Referenced by MRMTransitionGroup< SpectrumT, TransitionT >::subset().
◆ addScore()
◆ getFeature()
get a specified feature
Referenced by EmgScoring::calcElutionFitScore().
◆ getFeatureIDs()
| void getFeatureIDs | ( | std::vector< String > & | result | ) | const |
get a list of IDs of available features
◆ getFeatures()
| const std::vector<Feature>& getFeatures | ( | ) | const |
get a list of features
◆ getPrecursorFeature()
◆ getPrecursorFeatureIDs()
| void getPrecursorFeatureIDs | ( | std::vector< String > & | result | ) | const |
get a list of IDs of available precursor features
◆ getScore()
◆ getScores()
| const PGScoresType& getScores | ( | ) | const |
get all peakgroup scores
◆ operator=()
| MRMFeature& operator= | ( | const MRMFeature & | rhs | ) |
Assignment operator.
◆ setScores()
| void setScores | ( | const PGScoresType & | scores | ) |
set all peakgroup scores
Member Data Documentation
◆ feature_map_
|
protected |
map native ids to the features
◆ features_
|
protected |
◆ pg_scores_
|
protected |
peak group scores
◆ precursor_feature_map_
|
protected |
map native ids to the precursor features
◆ precursor_features_
|
protected |